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Merged
eladrion merged 10 commits into from
Feb 9, 2026
Merged

Factorize common workflow generation functionality. #147

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eceff13
Extrapolate basic functionality for workflow files generation into `S…
eladrion Dec 12, 2025
c92d089
[Fix/Refactor] Replace `getOutputTypes()` in `generateRuleInput()` wi…
eladrion Jan 8, 2026
0d583f0
[Refactor] Replace another append chain by string format.
eladrion Jan 8, 2026
6acff82
[Refactor] Remove unused function
eladrion Jan 8, 2026
84c898c
[FIX] Add missing Builder functionality for Snakemake
eladrion Jan 12, 2026
6da0e66
[FIX] Change variable names to CamelCase
eladrion Jan 12, 2026
8f149dd
[Refactor] Extrapolate preparation of output directory as separate me…
eladrion Jan 15, 2026
5b3e3ac
[Update] Extrapolate `getWorkflowName` and remove trailing prime symbol.
eladrion Jan 15, 2026
15fa60f
[FIX] Resolving import issues.
eladrion Feb 9, 2026
f31c83f
[FIX] Removing stale placeholder from logging info.
eladrion Feb 9, 2026
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166 changes: 90 additions & 76 deletions src/main/java/nl/uu/cs/ape/APE.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@
import java.nio.file.Path;
import java.util.*;


import org.json.JSONException;
import org.json.JSONObject;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
Expand Down Expand Up @@ -394,21 +393,23 @@ public static boolean writeSolutionToFile(SolutionsList allSolutions) throws IOE
* @return true if the execution was successfully performed, false otherwise.
*/
public static boolean writeExecutableWorkflows(SolutionsList allSolutions, boolean createPartialImplementations) {
Path executionsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Executables();
Integer noExecutions = allSolutions.getRunConfiguration().getNoExecutions();
if (executionsFolder == null || noExecutions == null || noExecutions == 0 || allSolutions.isEmpty()) {
if (allSolutions.isEmpty()) {
return false;
}
// Check the configuration before continuing.
APERunConfig runConfig = allSolutions.getRunConfiguration();
Path executionsFolder = runConfig.getSolutionDirPath2Executables();
int noExecutions = runConfig.getNoExecutions();
if (executionsFolder == null || noExecutions == 0) {
return false;
}

APEUtils.printHeader(null, "Executing first " + noExecutions + " solution");
APEUtils.timerStart("executingWorkflows", true);

final File executeDir = executionsFolder.toFile();
if (executeDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(executeDir, SolutionWorkflow.getFileNamePrefix(), "sh");
} else {
executeDir.mkdir();
}
/* Removing the existing files from the file system. */
prepareOutputDirectory(executionsFolder, "sh");

log.debug("Generating executable scripts.");

/* Creating the requested scripts in parallel. */
Expand Down Expand Up @@ -465,31 +466,33 @@ public static boolean writeDataFlowGraphs(SolutionsList allSolutions) {
* @return true if the generating was successfully performed, false otherwise.
*/
public static boolean writeDataFlowGraphs(SolutionsList allSolutions, RankDir orientation) {
Path graphsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Figures();
Integer noGraphs = allSolutions.getRunConfiguration().getNoGraphs();
if (graphsFolder == null || noGraphs == null || noGraphs == 0 || allSolutions.isEmpty()) {
return false;
}
if (allSolutions.isEmpty()) {
return false;
}
// Check the configuration before continuing.
APERunConfig runConfig = allSolutions.getRunConfiguration();
Path graphsFolder = runConfig.getSolutionDirPath2Figures();
int noGraphs = runConfig.getNoGraphs();
if (graphsFolder == null || noGraphs == 0) {
return false;
}
// Store whether we are in debug mode.
boolean debugMode = runConfig.getDebugMode();

APEUtils.printHeader(null, "Generating graphical representation",
"of the first " + noGraphs + " workflows");
APEUtils.timerStart("drawingGraphs", true);

/* Removing the existing files from the file system. */
File graphDir = graphsFolder.toFile();
if (graphDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(graphDir, SolutionWorkflow.getFileNamePrefix(), "png");
} else {
graphDir.mkdir();
}
/* Removing the existing files from the file system. */
prepareOutputDirectory(graphsFolder, "png");

log.debug("Generating data flow graphs (png).");
/* Creating the requested graphs in parallel. */
allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noGraphs).forEach(solution -> {
try {
String title = solution.getFileName();
Path path = graphsFolder.resolve(title);
solution.getDataflowGraph(title, orientation).write2File(path.toFile(), Format.PNG,
allSolutions.getRunConfiguration().getDebugMode());
solution.getDataflowGraph(title, orientation).write2File(path.toFile(), Format.PNG, debugMode);

} catch (IOException e) {
log.error("Error occurred while data flow graphs (png) to the file system.");
Expand Down Expand Up @@ -524,31 +527,32 @@ public static boolean writeTavernaDesignGraphs(SolutionsList allSolutions) {
* @return true if the generating was successfully performed, false otherwise.
*/
public static boolean writeTavernaDesignGraphs(SolutionsList allSolutions, Format format) {
Path graphsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Figures();
Integer noGraphs = allSolutions.getRunConfiguration().getNoGraphs();
if (graphsFolder == null || noGraphs == null || noGraphs == 0 || allSolutions.isEmpty()) {
return false;
}
if (allSolutions.isEmpty()) {
return false;
}
// Check the configuration before continuing.
APERunConfig runConfig = allSolutions.getRunConfiguration();
Path graphsFolder = runConfig.getSolutionDirPath2Figures();
int noGraphs = runConfig.getNoGraphs();
if (graphsFolder == null || noGraphs == 0) {
return false;
}
// Store whether we are in debug mode.
boolean debugMode = runConfig.getDebugMode();

APEUtils.printHeader(null, "Generating graphical representation",
"of the first " + noGraphs + " workflows");
APEUtils.timerStart("drawingGraphs", true);

/* Removing the existing files from the file system. */
File graphDir = graphsFolder.toFile();
if (graphDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(graphDir, SolutionWorkflow.getFileNamePrefix(), format.fileExtension);
} else {
graphDir.mkdir();
}
/* Removing the existing files from the file system. */
prepareOutputDirectory(graphsFolder, format.fileExtension);
log.debug("Generating data flow graphs (png).");
/* Creating the requested graphs in parallel. */
allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noGraphs).forEach(solution -> {
try {
String title = solution.getFileName();
Path path = graphsFolder.resolve(title);
solution.getTavernaStyleGraph(title).write2File(path.toFile(), format,
allSolutions.getRunConfiguration().getDebugMode());
solution.getTavernaStyleGraph(title).write2File(path.toFile(), format, debugMode);

} catch (IOException e) {
log.error("Error occurred while data flow graphs (png) to the file system.");
Expand Down Expand Up @@ -584,31 +588,32 @@ public static boolean writeControlFlowGraphs(SolutionsList allSolutions) {
* @return true if the generating was successfully performed, false otherwise.
*/
public static boolean writeControlFlowGraphs(SolutionsList allSolutions, RankDir orientation) {
Path graphsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Figures();
Integer noGraphs = allSolutions.getRunConfiguration().getNoGraphs();
if (graphsFolder == null || noGraphs == null || noGraphs == 0 || allSolutions.isEmpty()) {
if (allSolutions.isEmpty()) {
return false;
}
// Check the configuration before continuing.
APERunConfig runConfig = allSolutions.getRunConfiguration();
Path graphsFolder = runConfig.getSolutionDirPath2Figures();
int noGraphs = runConfig.getNoGraphs();
if (graphsFolder == null || noGraphs == 0) {
return false;
}
// Store whether we are in debug mode.
boolean debugMode = runConfig.getDebugMode();

APEUtils.printHeader(null, "Generating graphical representation",
"of the first " + noGraphs + " workflows");
APEUtils.timerStart("drawingGraphs", true);

/* Removing the existing files from the file system. */
File graphDir = graphsFolder.toFile();
if (graphDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(graphDir, SolutionWorkflow.getFileNamePrefix(), "png");
} else {
graphDir.mkdir();
}
prepareOutputDirectory(graphsFolder, "png");
log.debug("Generating control flow graphs (png).");
/* Creating the requested graphs in parallel. */
allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noGraphs).forEach(solution -> {
try {
String title = solution.getFileName();
Path path = graphsFolder.resolve(title);
solution.getControlflowGraph(title, orientation).write2File(path.toFile(), Format.PNG,
allSolutions.getRunConfiguration().getDebugMode());
solution.getControlflowGraph(title, orientation).write2File(path.toFile(), Format.PNG, debugMode);

} catch (IOException e) {
log.error("Error occurred while writing control flow graphs (png) to the file system.");
Expand All @@ -630,28 +635,23 @@ public static boolean writeControlFlowGraphs(SolutionsList allSolutions, RankDir
* @return true if the execution was successfully performed, false otherwise.
*/
public static boolean writeCWLWorkflows(SolutionsList allSolutions, boolean createPartialImplementations) {

if (allSolutions.isEmpty()) {
return false;
}
// Check the configuration before continuing.
Path cwlFolder = allSolutions.getRunConfiguration().getSolutionDirPath2CWL();
int noCWLFiles = allSolutions.getRunConfiguration().getNoCWL();
if (cwlFolder == null || noCWLFiles == 0 || allSolutions.isEmpty()) {
APERunConfig runConfig = allSolutions.getRunConfiguration();
Path cwlFolder = runConfig.getSolutionDirPath2CWL();
int noCWLFiles = runConfig.getNoCWL();
if (cwlFolder == null || noCWLFiles == 0) {
return false;
}

final String timerID = "writingCWL";
APEUtils.printHeader(null, String.format("Writing the first %d solution(s) to CWL files", noCWLFiles));
APEUtils.timerStart(timerID, true);

final File cwlDir = cwlFolder.toFile();
if (cwlDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(cwlDir, SolutionWorkflow.getFileNamePrefix(), "cwl");
} else {
// Create the CWL directory if it does not already exist
cwlDir.mkdir();
}
/* Removing the existing files from the file system. */
prepareOutputDirectory(cwlFolder, "cwl");
log.debug("Generating CWL files.");

// Write the CWL files
Expand Down Expand Up @@ -715,8 +715,10 @@ public static boolean writeSnakemakeWorkflows(SolutionsList allSolutions, boolea
if (allSolutions.isEmpty()) {
return false;
}
Path snakemakeFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Snakemake();
int noSnakemakeFiles = allSolutions.getRunConfiguration().getNoSnakemake();
// Check the configuration before continuing.
APERunConfig runConfig = allSolutions.getRunConfiguration();
Path snakemakeFolder = runConfig.getSolutionDirPath2Snakemake();
int noSnakemakeFiles = runConfig.getNoSnakemake();
if (snakemakeFolder == null || noSnakemakeFiles == 0) {
return false;
}
Expand All @@ -725,14 +727,8 @@ public static boolean writeSnakemakeWorkflows(SolutionsList allSolutions, boolea
APEUtils.printHeader(null, String.format("Writing the first %d solution(s) to Snakemake files", noSnakemakeFiles));
APEUtils.timerStart(timerID, true);

final File snakemakeDir = snakemakeFolder.toFile();
if (snakemakeDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(snakemakeDir, SolutionWorkflow.getFileNamePrefix(), "snakefile");
} else {
// Create the Snakemake directory if it does not already exist
snakemakeDir.mkdir();
}
/* Removing the existing files from the file system. */
prepareOutputDirectory(snakemakeFolder, "snakefile");
log.debug("Generating Snakemake files.");

allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noSnakemakeFiles).forEach(solution -> {
Expand Down Expand Up @@ -769,7 +765,25 @@ public static boolean writeSnakemakeWorkflows(SolutionsList allSolutions, boolea
return true;
}

/**
/**
* Prepares the output directory by removing all files with the given extension
* and creating the output directory if it does not exist.
*
* @param basePath The base path to create or clean up.
* @param fileExtension The extension of existing files to delete.
*/
public static void prepareOutputDirectory(Path basePath, String fileExtension) {
final File baseDir = basePath.toFile();
if (baseDir.isDirectory()) {
// If the directory already exists, empty it first
deleteExistingFiles(baseDir, SolutionWorkflow.getFileNamePrefix(), fileExtension);
} else {
baseDir.mkdir();
}
}


/**
* Delete all files in the given directory that start with the given prefix and
* have the given extension.
*
Expand Down
10 changes: 10 additions & 0 deletions src/main/java/nl/uu/cs/ape/configuration/APERunConfig.java
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Original file line number Diff line number Diff line change
Expand Up @@ -193,6 +193,7 @@ private APERunConfig(Builder builder) {
setNoExecutions(builder.noExecutions);
setNoGraphs(builder.noGraphs);
setNoCWL(builder.noCWL);
setNoSnakemake(builder.noSnakemake);
setUseWorkflowInput(builder.useWorkflowInput);
setUseAllGeneratedData(builder.useAllGeneratedData);
setDebugMode(builder.debugMode);
Expand Down Expand Up @@ -710,6 +711,8 @@ public interface IBuildStage {

IBuildStage withNoCWL(int noCWL);

IBuildStage withNoSnakemake(int noSnakemake);

IBuildStage withProgramInputs(List<Type> programInputs);

IBuildStage withProgramOutputs(List<Type> programOutputs);
Expand Down Expand Up @@ -741,6 +744,7 @@ public static final class Builder implements ISolutionMinLengthStage, ISolutionM
private int noExecutions;
private int noGraphs;
private int noCWL;
private int noSnakemake;
private List<Type> programInputs = Collections.emptyList();
private List<Type> programOutputs = Collections.emptyList();
private ConfigEnum useWorkflowInput;
Expand Down Expand Up @@ -817,6 +821,12 @@ public IBuildStage withNoCWL(int noCWL) {
return this;
}

@Override
public IBuildStage withNoSnakemake(int noSnakemake) {
this.noSnakemake = noSnakemake;
return this;
}

@Override
public IBuildStage withProgramInputs(List<Type> programInputs) {
this.programInputs = programInputs;
Expand Down
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